void OBBond::SetLength(double length)
{
OBAtom *atom1 = GetBeginAtom();
OBAtom *atom2 = GetEndAtom();
//split the length difference in half, and modify the bond twice
double firstLength = length + ((GetLength() - length) / 2);
SetLength(atom1, firstLength);
SetLength(atom2, length);
}
double OBBond::GetLength() const
{
double d2;
const OBAtom *begin, *end;
begin = GetBeginAtom();
end = GetEndAtom();
d2 = SQUARE(begin->GetX() - end->GetX());
d2 += SQUARE(begin->GetY() - end->GetY());
d2 += SQUARE(begin->GetZ() - end->GetZ());
return(sqrt(d2));
}
double OBBond::GetEquibLength() const
{
const OBAtom *begin, *end;
begin = GetBeginAtom();
end = GetEndAtom();
double length = CorrectedBondRad(begin->GetAtomicNum(), begin->GetHyb())
+ CorrectedBondRad(end->GetAtomicNum(), end->GetHyb());
if (IsAromatic())
return length * 0.93;
switch (_order) {
case 3:
return length * 0.87;
case 2:
return length * 0.91;
}
return length;
}
double OBBond::GetEquibLength() const
{
double length;
const OBAtom *begin, *end;
// CorrectedBondRad will always return a # now
// if (!CorrectedBondRad(GetBeginAtom(),rad1)) return(0.0);
// if (!CorrectedBondRad(GetEndAtom(),rad2)) return(0.0);
begin = GetBeginAtom();
end = GetEndAtom();
length = etab.CorrectedBondRad(begin->GetAtomicNum(), begin->GetHyb())
+ etab.CorrectedBondRad(end->GetAtomicNum(), end->GetHyb());
if (IsAromatic())
length *= 0.93;
else if (GetBO() == 2)
length *= 0.91;
else if (GetBO() == 3)
length *= 0.87;
return(length);
}